Commit Graph

9639 Commits

Author SHA1 Message Date
James Agnew 05defb58c5
Server fixes from Connectathon 32 (#4838)
* NPM test cleanup

* fix imports

* Ongoing cleanup

* Rework memory queue

* Reindex cleanup

* Cleanup

* Clean up

* Test fixes

* Test fixes

* Test fixes

* Test fix

* Test fix
2023-05-15 08:28:55 -04:00
James Agnew 483ddca3be
Transaction with delete then update should not fail (#4831)
* Fixed

* Test fixes

* Add test

* Ongoing work

* Work on xactx

* Cleanup

* Changelog cleanup

* Resolve fixme

* Rework broken APIs

* Version bump

* Add license headers

* License header update

* License

* rk on fixes

* Test fixes

* Address review comments

* Test fixes

* Add license headers

* License header
2023-05-15 07:41:40 -04:00
James Agnew 8cf14c8c0e
Dont crash indexing contained references on Bundle (#4881)
* Dont crash indexing contained references on Bundle

* Add changelog
2023-05-14 21:33:32 -04:00
Ken Stevens a308f60e16
relax (#4880)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-13 22:35:18 -04:00
Ken Stevens 4313dc9958
pointcut exceptions (#4822)
* enforce no exceptions on the invoking thread in PointCutLatch

* comment

* Msg.code

* Catch exceptions outside of await block

* fix migration issue

* Refactor PointcutLatch and add tests

* fix tests

* fix tests

* fix tests

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test

* fix test!

* fix test!

* fix test

* fix test

* clean up latch error formatting

* fix test

* fix test

* fix test

* fix test

* fix test

* fix tests

* fix test

* fix test

* Remove hapi-fhir-jpaserver-uhnfhirtest from build as it is crashing CI

* fix test

* fix intermittent

* A SNAPSHOT dependency on an upstream module was added to HAPI FHIR, which changed and caused some downstream tests to break.

* fix intermittent

* Add Maven enforcer plugin for CR dependencies

* Make maven enforcer conditional on CI builds

* Remove hapi-fhir-jpaserver-uhnfhirtest from build as it is crashing CI

* improve test logging

* pre-review cleanup

* review feedback

* remove hapi-fhir-base-test-jaxrsserver-kotlin from the build

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
2023-05-11 22:31:38 -04:00
JasonRoberts-smile 0475cb682f
Jr 20230502 fhir patch test coverage (#4841)
* add tests for fhir patch

* extract constants

* extract some methods

* isolate add operation

* isolate delete operation

* isolate replace operation

* isolate move operation

* clean up integer handling

* enumeration creation

* improve variable naming

* code review feedback
2023-05-11 16:40:57 -04:00
Tadgh 9d34e6b248
Credit for #4842 (#4865)
* Add credit

* Typo
2023-05-11 18:34:22 +00:00
Nicolai Gjøderum 679b809bf3
Fix: Replace basic field with empty value in TerserUtil (#4842)
* add test proving bug

* fix: handle empty fromValue in TerserUtil.replaceField

* add comment to TerserUtilTest.testReplaceFieldByEmptyValue
2023-05-10 20:09:43 -07:00
JP c052663561
Change to a release version of the Clinical Reasoning dependency. (#4858)
* A SNAPSHOT dependency on an upstream module was added to HAPI FHIR, which changed and caused some downstream tests to break.

* Add Maven enforcer plugin for CR dependencies

* Make maven enforcer conditional on CI builds
2023-05-10 20:25:42 +00:00
Ken Stevens 224b7f6206
SubscriptionTopic part3 (#4817)
* Force Verify tests

* wip

* merge troubleshooting rel_6_6 troubleshooting changes

* fix ITs (#4809)

* fix RestHookTestR5IT

* fix intermittent

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* post-merge cleanup

* fix test

* fix mock test

* fix wiring

* fix mock test

* fix test

* use IBaseResource.isDeleted()

* fixmes

* cleanup

* change log

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-09 16:29:21 -04:00
Tadgh e3545446eb
Mergeback of release into master branch (#4839)
* Force Verify tests

* fix ITs (#4809)

* fix RestHookTestR5IT

* fix intermittent

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Fix migrator error on Oracle (#4814)

* Fix Oracle SQL error

* Add changelog

* Update clinical reasoning version (#4816)

* Update clinical reasoning version

* Update version

* Update version

* Clean-up and more wireup of evaluationSettings

* Add changelog

---------

Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>

* Opening the care-gaps endpoint for GET. (#4823)

Co-authored-by: Chalma Maadaadi <chalma@alphora.com>

* added version to mdm golden resource tag (#4820)

Co-authored-by: Long Ma <long@smilecdr.com>

* Update the changelog for 4697 to be more descriptive (#4827)

* Update the changelog for 4697 to be more descriptive

* Futher tweaks of the changelog

* Fixes a bug with tags.  (#4813)

* Test, fix

* Drop constraint, add migration

* Add changelog

* Fix userSelected null vs false

* Fix merge

* Fix up checkstyle whining

* One more failure

* Fix test

* wip

* changelog clarity

Co-authored-by: James Agnew <jamesagnew@gmail.com>

* change index

---------

Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>

* fix migration issue (#4830)

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Create correct version enum

* Remove superfluous migration

* fixing test (#4835)

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

---------

Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: chalmarm <44471040+chalmarm@users.noreply.github.com>
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
2023-05-09 11:23:02 -07:00
Max Bureck 648d14c52c
Parser: Reporting unexpected repeating element for choice (#4574) (#4590)
* Parser: Reporting unexpected repeating element for choice (#4574)

IParserErrorHandler.unexpectedRepeatingElement is now also called for
unexpected repeating elements of type choice, where concrete names
may be different based on the choice's data type.

* setting test-utilities java version to the test version

* added changelog

* added Max to the developer liss

* removed unneeded dependency

---------

Co-authored-by: patrick-werner <pa.f.werner@gmail.com>
2023-05-08 20:42:25 +00:00
Dominique Villard 9ae71aba95
4379: allow interceptor annotation on methods (#4380)
* 4379: allow interceptor annotation on methods

* 4379: document order parameter when annotation set on method

* Credit for #4380

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-05-07 12:25:29 +00:00
James Agnew d5184a8a57
Don't generate empty JSON element for comment (#4832)
* Don't generate empty JSON element for comment

* Fixed
2023-05-06 16:05:48 -04:00
Tadgh 93f93d5e41
Add Migration Reviewer Workflow (#4828)
* Add new workflow

* Add some whitespace

* Empty spaces in non-migration file

* wip

* Tidy up workflow
2023-05-06 10:33:17 -07:00
Ken Stevens 17423e4831
fix migration issue (#4830)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-06 09:13:50 -07:00
Tadgh f0726a32d5
Fixes a bug with tags. (#4813)
* Test, fix

* Drop constraint, add migration

* Add changelog

* Fix userSelected null vs false

* Fix merge

* Fix up checkstyle whining

* One more failure

* Fix test

* wip

* changelog clarity

Co-authored-by: James Agnew <jamesagnew@gmail.com>

* change index

---------

Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-05-05 19:06:03 +00:00
Kevin Dougan SmileCDR c637cec622
4801 - Added new Index on HFJ_RESOURCE table (#4802)
* 4801 - Added new Index on HFJ_RESOURCE table.

* 4801 - Added new migration task for new Index on HFJ_RESOURCE table.

* Update hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceTable.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Applied review changes.

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-05-05 17:37:25 +00:00
Brenin Rhodes 87e8a810cd
Merge 4821 back to master (#4825)
* Merge 4821 into master

* Update to PRE3 snapshot
2023-05-05 08:50:53 -07:00
Ken Stevens 350d1a422c
merge release branch to master (#4811)
* Force Verify tests

* fix ITs (#4809)

* fix RestHookTestR5IT

* fix intermittent

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-05-03 19:51:43 +00:00
James Agnew a3c33d2a53
Add BasicAuditEventLogging (BALP) Interceptor (#4787)
* Begin work on BALP interceptor

* Work on BALP

* Basic profile

* Work on BALP

* Add BALP

* Work on balp

* Add update and delete

* Work on BALP

* Add logging

* Tests

* Modify test server

* Work on docs

* Add documentation

* Add changelog

* Fix #4728 - Typos in docs

* Test fixes

* Move changelog

* Update hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/interceptor/balp/BalpAuditCaptureInterceptor.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Resolve PR comments

* Test fixes

---------

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
2023-05-03 15:46:22 +00:00
Aleksej Parovysnik f4c0f6e9fc
#4468 fix previous link offset no cache pagination (#4489)
* #4468 Add test reproducing the issue

* #4468 Fix previous link for no cache offset pagination

* #4468 Use unchecked URI parsing

* Credit for #4489

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-05-02 12:49:36 +00:00
Zach Smith 9c1d235f90
Fix operation on nested type-choices in FhirPatch implementation (#4783)
* Fix operation on nested type-choices in FhirPatch implementation

* Add credit for #4783

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-05-01 09:52:34 +00:00
Tadgh 9a095cc2d7
version bump for next release (#4793)
* version bump

* Bump to correctnumber

* Version Enum and folder

* Remove interim from list

* wip
2023-04-30 15:01:28 -04:00
Luke deGruchy 79c96dc1bb
Port changes to master from release branch 6_4 (#4785)
* Start porting changes to master that were lost from the release branch.

* Add remainder of tag changes from release branch.

* Changelog changes.

* Fix schema migration.

* Remove duplicate lines.

* Update core to 6.0.1.

* Fixes for new core.

* Bump to snapshot 19 to mirror James' changes.

* Fix migration tasks.

* Fix some of the tests due to the core upgrade.

* Fix rest of tests.
2023-04-28 19:56:02 +00:00
michaelabuckley 81854baa02
Batch2 cleanup (#4779)
Post review batch2 cleanup.

Review fixes and cleanup from #4647

Deleted methods in IJobPersistence unused in prod paths, and replaced their usage in tests.
Lots of docs.
Replace copy-on-write pattern in JobDefinitionRegistry with simple ConcurrentHashMap
Fixed bad mappings from job ERRORED state to external APIs. People think ERRORED is a failed state. ¯\_(ツ)_/¯
Added some spec tests for chunk purging
Deprecated ERRORED. For deleting in 6.8
Lots of plans for 6.8. Too risky for 6.6
2023-04-28 15:44:30 -04:00
James Agnew e2e5ff6bb8
Version bump HAPI FHIR (#4788) 2023-04-28 19:30:51 +00:00
James Agnew 69a79e39a1
Subscription retriggering enhancements (#4758)
* Work on forward porting reindex optimize storage

* Subscription retriggering performance enhancements

* Adjust readmes

* Add a test

* Add test

* Cleanup

* Test cleanup

* Add comment

* Add changelogs

* Test fixes

* Test fixes

* Bump size

* Fixes

* Test logging

* Restore forkcount

* Test fix

* Test fix

* Version bump

* Clean up changelogs

* Address review comment
2023-04-28 12:06:38 -04:00
James Agnew 78ff58277a
Make inline resource storage use a better column type (#4763)
* Use text column on postgres

* Add changelog

* Test fix

* Merge
2023-04-28 12:06:27 -04:00
James Agnew e2717bd63a
Bump corelib to FHIR R5 Final (#4727)
* Core bump

* Build build issues

* Bump core

* Cleanup

* Cleanup

* Resolve intermittent

* Work on core

* Add failing test for a check

* Test fixes

* Fixes

* DOn't mangle subscriptions

* Fix

* License headers

* Build fixes

* Version bump

* Compile fixes

* Fix compile issues
2023-04-28 06:28:22 -04:00
longma1 2171ad04a2
3924 mdm match resources across partitions and storing golden resources on a specific partition (#4770)
* added mdm search all partition for golden resource functionality

* added mdm partition setting

* build header fix

* test fixes and added missing side effect of allowing cross partition links on opeartions

* added changelog, also test fixes

* fixed changelog to an actual yaml file

* review fixes,  also simplified tests

* reverted one test because the original test schenario was correct

* added setting clearing in afterEach method so test dont fail while run in maven

* bump to pre-15

---------

Co-authored-by: Long Ma <long@smilecdr.com>
2023-04-28 02:15:35 -06:00
David 457b39bac1
Fix $mdm clear doesn't expunge golden record resources (#4767)
* Failing test

* Add method to expunge collection of deleted resources

* Failing test passes

* Add changelog

* Version bump

* Forgot to commit change

* Update test

* Check type validity

* Fix broken tests

---------

Co-authored-by: David Chen <david.chen@smilecdr.com>
2023-04-27 21:35:27 -06:00
JasonRoberts-smile ae1e7400dd
delete operation removes element from list (#4782)
* delete operation removes element from list

* changelog
2023-04-28 00:01:28 +00:00
Tadgh 78b3b148ba
Support `_exportId` for bulk exports. (#4781)
* Full implementation, test, changelogs

* Add changelogs

* Add default method

* Update hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/export/WriteBinaryStep.java

Co-authored-by: James Agnew <jamesagnew@gmail.com>

* Code Review Comments

* Compilation failures

---------

Co-authored-by: James Agnew <jamesagnew@gmail.com>
2023-04-27 21:46:09 +00:00
James Agnew f9de5c918e
Apply fixes to review comments for #4772 (#4780)
* Add post-fetch filtering to bulk export

* Add changelog

* Add validator

* Test fixes

* Test fix

* Review comments for #4772

* Commit fix
2023-04-27 14:23:01 +00:00
markiantorno f6094eed47 removing backport tag from 4772 2023-04-27 08:22:13 -04:00
James Agnew 855e10a62d
Add post-fetch filtering to bulk export (#4772)
* Add post-fetch filtering to bulk export

* Add changelog

* Add validator

* Test fixes

* Test fix
2023-04-26 17:05:03 -04:00
Ken Stevens 6b9af3291e
R5 Subscriptions (#4748)
* comments from conversation with Gino

* rewrite R5 subscription canonicalization.  Expect the r5 subscription tests to fail now

* SubscriptionTopicR5Test passes now

* R4B tests pass now

* first two tests in RestHookTestR5Test now pass.  just need to convert the rest

* third test passes

* fourth test passes

* tests pass up to line 294

* wow what a marathon.  Turns out when we stripped the version we didn't remove it from the meta version.

* passes up to 427

* RestHookTestR5Test tests pass up to line 582

* RestHookTestR5Test tests pass up to line 591
Added SubscriptionTopicRegisteringSubscriber

* RestHookTestR5Test tests pass up to line 591
Added SubscriptionTopicRegisteringSubscriber

* RestHookTestR5Test tests pass up to line 636
Added SubscriptionTopicValidatingInterceptor

* RestHookTestR5Test tests pass up to line 689

* RestHookTestR5Test tests pass up to line 758

* 4 failures left

* woohoo all tests pass

* all tests pass and no PointCutLatch errors

* Msg.code

* changelog

* checkstyle

* fix some tests

* compile issue

* fix test

* fix regression

* fix test

* R5 currently runs tests in multiple threads, so change the sensitive one to an IT

* licenses

* review feedback

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-26 17:01:00 +00:00
michaelabuckley 8813d9beda
Batch stabilization (#4647)
* Use java event names for work chunk transitions.

* Cherry-pick d5ebd1f667 from rel_6_4

Avoid fetching work-chunk data (#4622)

* add end time to reduction step (#4640)

* add end time to reduction step

* add changelog

---------

Co-authored-by: Long Ma <long@smilecdr.com>
(cherry picked from commit 37f5e59ffc)

* Cancel processing

Provide error message in cancelled jobs, and avoid transitions in final states.

* Apply tx boundary to starting job and first chunk.

* cleanup

* Apply tx boundary to work chunk processing

* Delete BatchWorkChunk

* Introduce events for job create, and chunk dequeue

* Apply tx boundary to chunk handler

* Move instance cancellation to database

* tx boundary around stats collection and completion

* tx boundary around stats collection and completion

* Extend tx boundary to error, fail, and cancel

* Move failure into status calc

* ERROR is not an "ended" state.

* Revert generics cleanup to avoid noise

* Avoid sending gated chunks twice.

* Make no-data path safer.  Cleanup

* Fix mock test for step advance.

* Delete unsafe updateInstace() call

* Cleanup

* Changelog and notes

* Fix cancel boundary.  Cleanups

* Cleanup

* Sort mongo chunks for stable paging.

Other cleanup

* Document error handling

* Cleanup

* Update hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/Batch2JobHelper.java

Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>

---------

Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
2023-04-25 15:47:23 -07:00
Tadgh d6d2ff531f
4757 externalized binary npe (#4759)
* Basic test for reading from provider

* Basic test for reading from provider

* Failing test

* Add changelog

* Update hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/BinaryStorageInterceptorR4Test.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

---------

Co-authored-by: Ken Stevens <khstevens@gmail.com>
2023-04-25 18:34:27 +00:00
michaelabuckley 20c7a32203
Add covering data to res_link index for all tgt->src queries. (#4769)
Add covering data to res_link index for all tgt->src queries.
2023-04-24 23:24:11 +00:00
Tadgh 08c997c169
Compile CDR Master against specific HAPI Branch (#4768)
* Create new workflow

* Remove dead calls
2023-04-24 23:18:40 +00:00
Whiteiguana b7bc630500
4745 one source record should create no match link with no errors when two golden records are possible matches (#4765)
* created failing test for issue

* remove unused code from IT

* Fixed an issue where marking a golden resource as no match would fail.

---------

Co-authored-by: Steven Li <steven@smilecdr.com>
2023-04-24 14:38:40 -04:00
Brenin Rhodes 9670150f20
4697 - Add Clinical Reasoning Operations (#4722)
* Initial stub out of the CR repo API

* Pagination first pass

* Add HapiFhirRepository and Questionnaire operations

* Add services and providers for ActivityDefinition, PlanDefinition and QuestionnaireResponse

* Simplify the repo usage

* Simplified constructors

* Fix pom

* Setup service config

* Add test

* Add tests

* Add canonical and resource parameters to cr operations

* Add $questionnaire-package operation

* Remove services and cleanup beans

* Cleanup

* Add changelog

* Fix pom

* Add id parameter to extract

* Break out config by IG

* cleanup

* cleanup

* cleanup

* cleanup

* Add type level operations

* Move loadProvider call out of constructors with an EventListener annotation

* Cleanup package operation

* Update BaseCrR4Test.java

* cleanup

* cleanup

* Fix tests

* Fix test

* Fix $package arguments

* Remove $questionnaire-package

* Add r5 apply operation name

* Remove config

* cleanup

* cleanup

* cleanup

* cleanup

* Comment out failing tests.  Fix coming in another branch.

* Fix config for 1.3 cql measure tests

* Fix checkstyle

* Change measure service config to resolve intermittent test issues

---------

Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
2023-04-24 14:37:55 -04:00
TipzCM 1c0addafeb
transaction bundle multi-threading issues (#4739)
* a solution for trying to avoid multi-thread issues for transaction bundle processing

* cleanup

* using retries

* mnor tweaks

* checking in

* changes

* updating changelog

* some minor tweaks

* cleanup

* flip if

---------

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-20 18:43:37 +00:00
Ken Stevens 58850fed82
try removing fork count from surefire (#4752)
* try removing fork count from test-r4

* try removing fork count from the rest of the projects

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-20 13:58:35 -04:00
Qingyixia 55613a9bf2
Fixed the Null Pointer Exception on mdm-submit operation (#4751)
* Fixed the Null Pointer Exception on mdm-submit operation

* Addressing suggestion
2023-04-19 12:24:39 -07:00
Qingyixia 6eafd3fe5d
The Lenient error handler will now throw exceptions when encode invalid extension containing value and nested extensions (#4747)
* The Lenient error handler will throw exceptions when encode invalid extension containing value and nested extensions

* Addressing suggestions

* Minor changes

* Minor fix
2023-04-18 13:59:23 -04:00
Ken Stevens 9e741cb145
remove enabled flag and instead only create the subscription topic beans in the fhir versions that use them (#4737)
Co-authored-by: Ken Stevens <ken@smilecdr.com>
2023-04-18 10:20:43 -04:00
samguntersmilecdr 396007af40
test + change + changelog (#4732) 2023-04-18 09:25:15 -04:00